The effects of introduced biocontrol microbes on root and flower surface microbiomes of strawberry grown in coir substrate in a polythene tunnel

Abstract Aims Biocontrol of plant diseases is a key component of sustainable agriculture. Augmented introduction of biocontrol microbes may affect the resident phytobiome, potentially leading to unintended consequences. We studied the effects of three biocontrol microbes (Gliocladium catenulatum, Trichoderma asperellum, and Bacillus subtilis) on communities of living microbes on table-top strawberries grown in coir bags in a polythene tunnel. Methods and results Gliocladium catenulatum and T. asperellum were applied to roots via drenching soon after planting, and G. catenulatum and B. subtilis were sprayed onto flowers. To profile communities of living microbes, we treated samples with PMAxx™ before DNA extraction. Flower and root epiphytes were profiled by amplicon and shot-gun sequencing, respectively. Applying the three microbes led to significant increases in their relative abundance on both flowers and roots. The two introduced fungal taxa (G. catenulatum and T. asperellum) appeared to affect mainly fungal microbiome components, whereas the introduced bacterial taxon (B. subtilis) mainly affected bacterial microbiome components. The effects of introduced biocontrol microbes on the resident microbiome were more profound and long-lasting on roots than on flowers. Conclusions Introduced microbes can persist better on roots than on flowers. Although the applied microbes led to significant changes in the overall microbial composition, their effects on individual taxa groups were limited. Introduced microbes appeared to have only largely affected microbial communities in the same kingdom.